Error in CFDEM coupling using the latest OpenFOAM 5.x

Submitted by Rachel on Fri, 12/08/2017 - 06:17

Dear all, I have just installed the newest version of CFDEM 3.8.0 and can run the tutorial example successfully. However, when I am running a code of myself, I run into the error below. I attached my log file so that you may know how to fix this problem:

// run_parallel_cfdemSolverPiso_ErgunTestMPI_CFDDEM //

/home/Rachel/CFDEM/CFDEMcoupling-PUBLIC-5.x/tutorials/cfdemSolverPiso/ErgunTestMPI_1206/CFD

/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 5.x |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 5.x-529d4137e100
Exec : cfdemSolverPiso -parallel
Date : Dec 07 2017
Time : 22:04:39
Host : "Rachel"
PID : 15225
I/O : uncollated
Case : /home/Rachel/CFDEM/CFDEMcoupling-PUBLIC-5.x/tutorials/cfdemSolverPiso/ErgunTestMPI_1206/CFD
nProcs : 2
Slaves : 1("Rachel.15226")
Pstream initialized with:
floatTransfer : 0
nProcsSimpleSum : 0
commsType : nonBlocking
polling iterations : 0
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0

PISO: Operating solver in PISO mode

Reading field p

Reading physical velocity field U
Note: only if voidfraction at boundary is 1, U is superficial velocity!!!

Reading momentum exchange field Ksl

Reading voidfraction field voidfraction = (Vgas/Vparticle)

Creating density field rho

Reading particle velocity field Us

Reading/calculating face flux field phi

Generating interstitial face flux field phiByVoidfraction

Selecting incompressible transport model Newtonian
Selecting turbulence model type laminar
Selecting laminar stress model Stokes
No finite volume options present

Reading g
Selecting locateModel engine
Selecting dataExchangeModel twoWayMPI
Starting up LIGGGHTS for first time execution
Executing input script '../DEM/in.liggghts_run'
LIGGGHTS (Version LIGGGHTS-PUBLIC 3.8.0, compiled 2017-12-07-21:41:03 by Rachel, git commit 3fb80baf0d562d3b6cea96e4f39afc94af4a4293)
log ../DEM/log.liggghts
thermo_log ../DEM/post/thermo.txt
......
......
......
Resetting global state of Fix contacthistory Style contacthistory from restart file info
Resetting per-atom state of Fix contacthistory Style contacthistory from restart file info
Setting up run at Thu Dec 7 22:04:39 2017

Import and parallelization of mesh bottomwall containing 2 triangle(s) successful
Import and parallelization of mesh leftwall containing 2 triangle(s) successful
Import and parallelization of mesh rightwall containing 2 triangle(s) successful
Import and parallelization of mesh frontwall containing 2 triangle(s) successful
Import and parallelization of mesh backwall containing 2 triangle(s) successful
Import and parallelization of mesh topwall_delete containing 2 triangle(s) successful
Memory usage per processor = 42.2335 Mbytes
Step Atoms KinEng 1 Volume tscheck[ tscheck[ centerOf explDrag explDrag explDrag cfd2[1] cfd2[2] cfd2[3]
3000001 40000 6.5828649e-08 9.3877256e-07 0.027 0 0 0.049916519 0 0 0 0 0 0
Loop time of 2.86102e-06 on 2 procs for 0 steps with 40000 atoms, finish time Thu Dec 7 22:04:39 2017

Pair time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0 (0)
Outpt time (%) = 0 (0)
Other time (%) = 2.86102e-06 (100)

Nlocal: 20000 ave 20074 max 19926 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 2446.5 ave 2487 max 2406 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 130952 ave 131231 max 130672 min
Histogram: 1 0 0 0 0 0 0 0 0 1

Total # of neighbors = 261903
Ave neighs/atom = 6.54758
Neighbor list builds = 0
Dangerous builds = 0

#write_restart ../DEM/post/restart/liggghts_triaxial.restart

Selecting IOModel basicIO
Selecting probeModel off
Selecting voidFractionModel divided
Selecting averagingModel dense
Selecting clockModel standardClock
start clock measurement at t >0.0001
Selecting smoothingModel off
Selecting meshMotionModel noMeshMotion

CFDEMcoupling version: cfdem-3.8.1
, compatible to LIGGGHTS version: 3.8.0
, compatible to OF version and build: 5.x-commit-538044ac05c4672b37c7df607dca1116fa88df88

You are currently using:
OF version: 5.x
OF build: 5.x-529d4137e100
CFDEM build: 3.8.0-3-gb237264

cg is set to: 1
LIGGGHTS hosts 3 atom types.
If BC are important, please provide volScalarFields -imp/expParticleForces-
ignoring ddt(voidfraction)
Selecting momCoupleModel implicitCouple

implicit momentum exchange field calculate if alphaP larger than : 1
Selecting forceModel DiFeliceDrag
Selecting forceSubModel ImEx
reading switches:
looking for treatForceExplicit ... not found in dict, using default. treatForceExplicit = false
looking for implForceDEM ... not found in dict, using default. implForceDEM = false
looking for verbose ... not found in dict, using default. verbose = false
looking for interpolation ... found in dict. interpolation = true
looking for scalarViscosity ... not found in dict, using default. scalarViscosity = false

Selecting forceModel gradPForce
Selecting forceSubModel ImEx
reading switches:
looking for treatForceExplicit ... not found in dict, using default. treatForceExplicit = true
looking for verbose ... not found in dict, using default. verbose = false
looking for interpolation ... found in dict. interpolation = true

Selecting forceModel viscForce
Selecting forceSubModel ImEx
reading switches:
looking for treatForceExplicit ... not found in dict, using default. treatForceExplicit = true
looking for verbose ... not found in dict, using default. verbose = false
looking for interpolation ... found in dict. interpolation = true
looking for scalarViscosity ... not found in dict, using default. scalarViscosity = false

Selecting forceModel fieldStore
Creating field stored_U
Selecting liggghtsCommandModel runLiggghts ,provide dicts, numbered from 0 to n
Selecting liggghtsCommandModel execute ,provide dicts, numbered from 0 to n
liggghtsCommand delete_atoms region deleteArea compress yes
Selecting liggghtsCommandModel writeLiggghts ,provide dicts, numbered from 0 to n
writeLiggghts: A restart file writeName_write_restart ../DEM/post/restart/liggghts.restartCFDEM is written.
solving volume averaged Navier Stokes equations of type A
check if Archimedes lift is necessary (depends on pressure formulation)

Starting time loop

--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[0]
[0]
[0] --> FOAM FATAL IO ERROR:
[0] 'functions' entry is not a dictionary
[0]
[0] file: /home/Rachel/CFDEM/CFDEMcoupling-PUBLIC-5.x/tutorials/cfdemSolverPiso/ErgunTestMPI_1206/CFD/system/controlDict from line 18 to line 222.
[0]
[0] From function bool Foam::functionObjectList::read()
[0] in file db/functionObjects/functionObjectList/functionObjectList.C at line 586.
[0]
FOAM parallel run exiting
[0]
[1]
[1]
[1] --> FOAM FATAL IO ERROR:
[1] 'functions' entry is not a dictionary
[1]
[1] file: IOstream from line 0 to line 0.
[1]
[1] From function bool Foam::functionObjectList::read()
[1] in file db/functionObjects/functionObjectList/functionObjectList.C at line 586.
[1]
FOAM parallel run exiting
[1]
[Rachel:15222] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[Rachel:15222] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

alice's picture

alice | Wed, 01/10/2018 - 07:31

Hi rachel,

sorry, just saw this now. Please have a look at the tutorials that come with CFDEM(R)coupling, the syntax of the probes changed slightly (system/controlDict).

Best,

Alice

federicogaspar@... | Thu, 02/15/2018 - 19:21

Hi all! I get a similar error message from the log file (looking for treatForceExplicit ... not found in dict, using default. treatForceExplicit = false
). I compared system/controlDict file in order to avoid syntax changes from different versions (the simulation was set up in another pc).

.....

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